Multiple sequence alignment - TraesCS5B01G149800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G149800 chr5B 100.000 3945 0 0 1 3945 278009276 278013220 0.000000e+00 7286.0
1 TraesCS5B01G149800 chr5D 90.561 3814 201 64 230 3943 244621790 244625544 0.000000e+00 4902.0
2 TraesCS5B01G149800 chr5D 92.000 250 14 2 1 244 244621528 244621777 2.920000e-91 346.0
3 TraesCS5B01G149800 chr5D 93.204 103 4 1 2590 2692 250069618 250069717 8.830000e-32 148.0
4 TraesCS5B01G149800 chr5A 90.491 3197 179 51 1 3137 328802119 328805250 0.000000e+00 4104.0
5 TraesCS5B01G149800 chr5A 95.898 707 17 5 3239 3945 328807103 328807797 0.000000e+00 1134.0
6 TraesCS5B01G149800 chr5A 91.346 104 8 1 2585 2687 698639622 698639725 1.480000e-29 141.0
7 TraesCS5B01G149800 chr3B 82.636 478 77 6 3412 3886 597547158 597546684 6.100000e-113 418.0
8 TraesCS5B01G149800 chr3B 79.630 270 42 8 430 696 446631185 446630926 8.710000e-42 182.0
9 TraesCS5B01G149800 chr3B 82.081 173 25 4 2096 2263 7346627 7346456 4.110000e-30 143.0
10 TraesCS5B01G149800 chr3D 82.008 478 80 6 3412 3886 454747753 454747279 6.140000e-108 401.0
11 TraesCS5B01G149800 chr3D 80.531 226 28 10 2050 2260 443422349 443422573 4.080000e-35 159.0
12 TraesCS5B01G149800 chr3D 100.000 32 0 0 2050 2081 443365064 443365095 4.260000e-05 60.2
13 TraesCS5B01G149800 chr3A 82.008 478 80 6 3412 3886 596796029 596795555 6.140000e-108 401.0
14 TraesCS5B01G149800 chr3A 81.818 242 35 9 456 693 456925837 456926073 1.120000e-45 195.0
15 TraesCS5B01G149800 chr2B 86.957 207 23 4 485 690 693886515 693886718 3.070000e-56 230.0
16 TraesCS5B01G149800 chr2B 82.407 216 18 14 2096 2304 331023458 331023256 1.880000e-38 171.0
17 TraesCS5B01G149800 chr2B 81.279 219 25 9 2050 2254 66667769 66667985 3.150000e-36 163.0
18 TraesCS5B01G149800 chr7A 85.854 205 25 3 493 696 342763626 342763425 8.590000e-52 215.0
19 TraesCS5B01G149800 chr7A 81.776 214 27 5 484 696 558674924 558675126 6.780000e-38 169.0
20 TraesCS5B01G149800 chr2D 82.648 219 20 13 2091 2304 218020726 218020931 1.130000e-40 178.0
21 TraesCS5B01G149800 chr2D 95.556 90 4 0 2598 2687 331544237 331544148 1.140000e-30 145.0
22 TraesCS5B01G149800 chr2D 92.929 99 6 1 2600 2697 15192879 15192977 4.110000e-30 143.0
23 TraesCS5B01G149800 chr1D 79.926 269 31 15 2053 2308 102775139 102774881 4.050000e-40 176.0
24 TraesCS5B01G149800 chr1A 81.776 214 23 10 2053 2253 102169136 102169346 8.770000e-37 165.0
25 TraesCS5B01G149800 chr1A 87.826 115 11 2 2589 2703 427520594 427520483 8.890000e-27 132.0
26 TraesCS5B01G149800 chr1B 78.967 271 34 15 2053 2310 158310888 158310628 3.150000e-36 163.0
27 TraesCS5B01G149800 chr6A 96.591 88 3 0 2603 2690 610350314 610350227 3.180000e-31 147.0
28 TraesCS5B01G149800 chr6D 92.079 101 6 2 2603 2703 59623259 59623161 1.480000e-29 141.0
29 TraesCS5B01G149800 chr6D 75.897 195 43 3 3519 3711 452497322 452497514 3.240000e-16 97.1
30 TraesCS5B01G149800 chr6D 90.411 73 6 1 571 643 471489761 471489832 1.170000e-15 95.3
31 TraesCS5B01G149800 chr4B 88.288 111 13 0 2153 2263 581308458 581308348 2.470000e-27 134.0
32 TraesCS5B01G149800 chr6B 80.255 157 18 9 2050 2198 711383523 711383674 5.390000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G149800 chr5B 278009276 278013220 3944 False 7286 7286 100.0000 1 3945 1 chr5B.!!$F1 3944
1 TraesCS5B01G149800 chr5D 244621528 244625544 4016 False 2624 4902 91.2805 1 3943 2 chr5D.!!$F2 3942
2 TraesCS5B01G149800 chr5A 328802119 328807797 5678 False 2619 4104 93.1945 1 3945 2 chr5A.!!$F2 3944

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
66 67 0.039180 TGGAGGCTGAGACGTCCTTA 59.961 55.0 13.01 0.0 43.52 2.69 F
386 423 0.319555 CGAGACTTCAGGCGGAACAA 60.320 55.0 0.00 0.0 0.00 2.83 F
1172 1261 0.533755 ACCTCCATATCAGCAAGCGC 60.534 55.0 0.00 0.0 38.99 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1353 1.628846 GTTCTCCTAGGGTTGAAGCCA 59.371 52.381 16.56 0.95 38.48 4.75 R
1459 1549 1.671054 GCCAAAGCAGCCTACGTGA 60.671 57.895 0.00 0.00 39.53 4.35 R
3092 3235 1.348064 AGGAGAAATGGTGTCGGTCA 58.652 50.000 0.00 0.00 0.00 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.039180 TGGAGGCTGAGACGTCCTTA 59.961 55.000 13.01 0.00 43.52 2.69
81 82 0.753111 CCTTAGCACCATTGGAGGCC 60.753 60.000 10.37 0.00 0.00 5.19
217 224 2.290071 GCTGTTGTTAGCTAGTGGGGAA 60.290 50.000 0.00 0.00 40.52 3.97
317 354 9.809395 AACTCTAGTAGATGCTGTATATTACCA 57.191 33.333 0.00 0.00 0.00 3.25
322 359 6.959954 AGTAGATGCTGTATATTACCATCCCA 59.040 38.462 0.00 0.00 34.35 4.37
344 381 0.465460 AAACCAGTTTGCGGCTCTCA 60.465 50.000 0.00 0.00 0.00 3.27
352 389 2.543777 TTGCGGCTCTCACTAAAACT 57.456 45.000 0.00 0.00 0.00 2.66
386 423 0.319555 CGAGACTTCAGGCGGAACAA 60.320 55.000 0.00 0.00 0.00 2.83
415 452 5.460419 CGCAAACCTGTACTGCAAATTTTTA 59.540 36.000 5.08 0.00 35.78 1.52
463 500 2.665185 GATCCCGCATGGTACCGC 60.665 66.667 7.57 4.44 34.77 5.68
469 506 0.949105 CCGCATGGTACCGCTAATCC 60.949 60.000 7.57 0.00 0.00 3.01
712 789 2.223377 GGAAGCGATTTATAACCTGGCG 59.777 50.000 0.00 0.00 0.00 5.69
717 794 2.546789 CGATTTATAACCTGGCGGGAAC 59.453 50.000 21.81 0.00 38.76 3.62
736 813 0.846693 CCAAGGTCCCCATTCCCTAG 59.153 60.000 0.00 0.00 0.00 3.02
743 820 1.431633 TCCCCATTCCCTAGAGCGATA 59.568 52.381 0.00 0.00 0.00 2.92
787 864 5.051816 TCGCTAAACCGATATAAACCCTTG 58.948 41.667 0.00 0.00 31.36 3.61
788 865 4.812626 CGCTAAACCGATATAAACCCTTGT 59.187 41.667 0.00 0.00 0.00 3.16
789 866 5.984926 CGCTAAACCGATATAAACCCTTGTA 59.015 40.000 0.00 0.00 0.00 2.41
790 867 6.145048 CGCTAAACCGATATAAACCCTTGTAG 59.855 42.308 0.00 0.00 0.00 2.74
791 868 6.073385 GCTAAACCGATATAAACCCTTGTAGC 60.073 42.308 0.00 0.00 0.00 3.58
792 869 5.625568 AACCGATATAAACCCTTGTAGCT 57.374 39.130 0.00 0.00 0.00 3.32
793 870 4.957296 ACCGATATAAACCCTTGTAGCTG 58.043 43.478 0.00 0.00 0.00 4.24
794 871 4.202326 ACCGATATAAACCCTTGTAGCTGG 60.202 45.833 0.00 0.00 0.00 4.85
852 929 1.670674 CGGCATTTTGCTGCAATGAGT 60.671 47.619 16.77 0.00 43.46 3.41
909 989 0.824595 TCACGAACTCCCTCGGAACA 60.825 55.000 0.00 0.00 43.22 3.18
923 1003 1.055849 GGAACAACAGGGCCCAAATT 58.944 50.000 27.56 12.33 0.00 1.82
925 1005 0.764271 AACAACAGGGCCCAAATTGG 59.236 50.000 27.56 10.68 37.25 3.16
951 1031 1.566298 AAGCCAGTCCCACATCTCCC 61.566 60.000 0.00 0.00 0.00 4.30
954 1034 2.365635 AGTCCCACATCTCCCCCG 60.366 66.667 0.00 0.00 0.00 5.73
1172 1261 0.533755 ACCTCCATATCAGCAAGCGC 60.534 55.000 0.00 0.00 38.99 5.92
1190 1279 1.728971 CGCTGCTCGTTCATTTCTCTT 59.271 47.619 0.00 0.00 0.00 2.85
1193 1282 3.061965 GCTGCTCGTTCATTTCTCTTCTC 59.938 47.826 0.00 0.00 0.00 2.87
1195 1284 4.825422 TGCTCGTTCATTTCTCTTCTCAT 58.175 39.130 0.00 0.00 0.00 2.90
1205 1294 3.961480 TCTCTTCTCATTTCGGCTTCA 57.039 42.857 0.00 0.00 0.00 3.02
1212 1301 3.260884 TCTCATTTCGGCTTCACCTTACT 59.739 43.478 0.00 0.00 35.61 2.24
1264 1353 5.612725 ATGTGGTGGTTTCAACTTCAAAT 57.387 34.783 0.00 0.00 0.00 2.32
1352 1442 2.029290 AGGCGTTCTGTCGTTGACTTAT 60.029 45.455 0.00 0.00 33.15 1.73
1396 1486 3.435327 CCTGCAAATTACTGTGCGTCTTA 59.565 43.478 0.00 0.00 43.93 2.10
1462 1552 8.654230 ATGTGTCTTCATATCTGTAATGTCAC 57.346 34.615 0.00 0.00 0.00 3.67
1558 1648 6.847421 TGATGAGTATGGATCTACAGATGG 57.153 41.667 0.00 0.00 34.37 3.51
1610 1700 7.936026 ATTATTTTCAGGGGGCATTATTCTT 57.064 32.000 0.00 0.00 0.00 2.52
1729 1821 3.845781 CTGTGCCTCAGGTATTGGTAT 57.154 47.619 0.00 0.00 40.23 2.73
1730 1822 4.156455 CTGTGCCTCAGGTATTGGTATT 57.844 45.455 0.00 0.00 40.23 1.89
1731 1823 3.879295 CTGTGCCTCAGGTATTGGTATTG 59.121 47.826 0.00 0.00 40.23 1.90
1744 1836 8.499406 AGGTATTGGTATTGGTATTGCTTCTAA 58.501 33.333 0.00 0.00 0.00 2.10
1749 1841 8.771920 TGGTATTGGTATTGCTTCTAATATCG 57.228 34.615 0.00 0.00 0.00 2.92
1782 1874 9.337091 ACACATTCACGTACATAAATTTTAAGC 57.663 29.630 0.00 0.00 0.00 3.09
1789 1881 7.218204 CACGTACATAAATTTTAAGCAAGAGGC 59.782 37.037 0.00 0.00 45.30 4.70
1800 1892 3.492102 AGCAAGAGGCAACACTTTCTA 57.508 42.857 0.00 0.00 45.85 2.10
1935 2041 1.086696 CAAGTTATGCACGGGTGGAG 58.913 55.000 0.43 0.00 33.50 3.86
1952 2058 4.569865 GGTGGAGTGAATTATTGACCCCTT 60.570 45.833 0.00 0.00 0.00 3.95
1959 2065 4.097741 TGAATTATTGACCCCTTTCATGCG 59.902 41.667 0.00 0.00 0.00 4.73
1964 2074 1.648467 GACCCCTTTCATGCGCTGTC 61.648 60.000 9.73 0.00 0.00 3.51
1970 2080 2.938451 CCTTTCATGCGCTGTCAGATTA 59.062 45.455 9.73 0.00 0.00 1.75
1975 2085 2.125461 TGCGCTGTCAGATTATCTCG 57.875 50.000 9.73 0.00 0.00 4.04
2001 2111 4.508461 TGAGCATCATGGTTTGAACTTG 57.492 40.909 0.00 0.00 42.56 3.16
2002 2112 3.890756 TGAGCATCATGGTTTGAACTTGT 59.109 39.130 0.00 0.00 42.56 3.16
2003 2113 4.022935 TGAGCATCATGGTTTGAACTTGTC 60.023 41.667 0.00 0.00 42.56 3.18
2005 2115 4.022589 AGCATCATGGTTTGAACTTGTCTG 60.023 41.667 0.00 0.00 38.03 3.51
2006 2116 4.261741 GCATCATGGTTTGAACTTGTCTGT 60.262 41.667 0.00 0.00 38.03 3.41
2007 2117 5.455392 CATCATGGTTTGAACTTGTCTGTC 58.545 41.667 0.00 0.00 38.03 3.51
2022 2132 6.822667 TTGTCTGTCAAGCATTACAATCAT 57.177 33.333 0.00 0.00 31.86 2.45
2034 2144 7.709269 GCATTACAATCATCATGCTGATTTT 57.291 32.000 19.55 16.44 41.89 1.82
2035 2145 8.806177 GCATTACAATCATCATGCTGATTTTA 57.194 30.769 19.55 15.55 41.89 1.52
2133 2245 7.148373 GCCATGTCTATGACAAAAATTGCAAAT 60.148 33.333 1.71 0.00 45.96 2.32
2294 2413 8.749354 ACCTAGAACTTCATTTGTTTTGAAACT 58.251 29.630 7.97 0.00 39.59 2.66
2304 2423 6.445357 TTTGTTTTGAAACTGAGGGAGTAC 57.555 37.500 7.97 0.00 39.59 2.73
2321 2462 9.152595 GAGGGAGTACTTTTAACATACTGAAAG 57.847 37.037 0.00 0.00 42.29 2.62
2350 2491 2.849942 TGCTGCTAGCTTTTGAGACAA 58.150 42.857 17.23 0.00 42.97 3.18
2351 2492 3.213506 TGCTGCTAGCTTTTGAGACAAA 58.786 40.909 17.23 0.00 42.97 2.83
2366 2507 4.202000 TGAGACAAAGCATGCGAAAAGAAA 60.202 37.500 13.01 0.00 0.00 2.52
2367 2508 4.681744 AGACAAAGCATGCGAAAAGAAAA 58.318 34.783 13.01 0.00 0.00 2.29
2370 2511 6.922957 AGACAAAGCATGCGAAAAGAAAATTA 59.077 30.769 13.01 0.00 0.00 1.40
2399 2540 8.677148 AAAAATATACGATGTAGGTGCTGATT 57.323 30.769 0.00 0.00 0.00 2.57
2451 2592 5.978919 TGTAGTTTTGATGCAAAAGAAGCAG 59.021 36.000 5.64 0.00 46.36 4.24
2556 2697 6.265304 AGAGGTGAGTAGAATAGAAGGGTTT 58.735 40.000 0.00 0.00 0.00 3.27
2570 2711 2.929301 AGGGTTTGATGGGAACTAGGA 58.071 47.619 0.00 0.00 0.00 2.94
2952 3095 1.619654 TTTGTGGCTTGACCCATCTG 58.380 50.000 0.00 0.00 37.20 2.90
2980 3123 2.290260 TGTGGAGCCTGGAGTTATGTTG 60.290 50.000 0.00 0.00 0.00 3.33
3067 3210 5.234543 GCTTATTGTACAGCTAGCCAAGTAC 59.765 44.000 24.59 24.59 37.82 2.73
3068 3211 6.540438 TTATTGTACAGCTAGCCAAGTACT 57.460 37.500 28.14 18.63 38.09 2.73
3069 3212 7.649533 TTATTGTACAGCTAGCCAAGTACTA 57.350 36.000 28.14 24.30 38.09 1.82
3092 3235 3.728385 AGCCAGGTAGATCTTTTTGCT 57.272 42.857 0.00 0.40 0.00 3.91
3146 3315 2.618709 GTGGCTGGTGGTAAATGATAGC 59.381 50.000 0.00 0.00 0.00 2.97
3164 3552 9.838339 AATGATAGCTGTACTTTATTTAGCACT 57.162 29.630 0.00 0.00 36.87 4.40
3187 3575 9.088512 CACTACTAAGATTGATTTCAGTGTACC 57.911 37.037 0.00 0.00 0.00 3.34
3281 5178 9.424319 TCTGACTGAAAAGTATCTGAATTACAC 57.576 33.333 0.00 0.00 0.00 2.90
3619 5516 1.078426 CCTCATTGGTGGGTCGTCC 60.078 63.158 0.00 0.00 0.00 4.79
3832 5729 2.816958 CGGCTCACATTCTGCGCT 60.817 61.111 9.73 0.00 0.00 5.92
3877 5774 3.384532 GCGGGGAAGTCGGTGGTA 61.385 66.667 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.431131 CCGGCCTCCAATGGTGCT 62.431 66.667 14.12 0.00 0.00 4.40
81 82 0.940126 GCATGTCATGGCTTCTACCG 59.060 55.000 14.64 0.00 0.00 4.02
203 204 3.071023 CGGATGAATTCCCCACTAGCTAA 59.929 47.826 2.27 0.00 42.06 3.09
217 224 4.102210 ACTGTCAAGATCCATCGGATGAAT 59.898 41.667 19.30 4.18 43.27 2.57
225 232 4.701765 ACATAGCACTGTCAAGATCCATC 58.298 43.478 0.00 0.00 0.00 3.51
299 336 6.728632 TGTGGGATGGTAATATACAGCATCTA 59.271 38.462 20.30 12.20 45.72 1.98
314 351 2.433970 CAAACTGGTTTTGTGGGATGGT 59.566 45.455 0.00 0.00 39.96 3.55
317 354 2.908688 GCAAACTGGTTTTGTGGGAT 57.091 45.000 0.00 0.00 45.70 3.85
322 359 0.102300 GAGCCGCAAACTGGTTTTGT 59.898 50.000 0.00 0.00 45.70 2.83
344 381 5.163893 CGTGATACCGCAAATCAGTTTTAGT 60.164 40.000 0.00 0.00 34.12 2.24
352 389 2.165641 AGTCTCGTGATACCGCAAATCA 59.834 45.455 0.00 0.00 0.00 2.57
386 423 0.881118 CAGTACAGGTTTGCGGCATT 59.119 50.000 2.28 0.00 0.00 3.56
425 462 4.996113 CGGAACATATGCCGCAAC 57.004 55.556 8.56 0.00 41.17 4.17
445 482 2.355837 CGGTACCATGCGGGATCG 60.356 66.667 13.54 0.00 41.15 3.69
690 767 3.211045 GCCAGGTTATAAATCGCTTCCA 58.789 45.455 0.00 0.00 0.00 3.53
691 768 2.223377 CGCCAGGTTATAAATCGCTTCC 59.777 50.000 0.00 0.00 0.00 3.46
693 770 2.218603 CCGCCAGGTTATAAATCGCTT 58.781 47.619 0.00 0.00 0.00 4.68
695 772 0.872388 CCCGCCAGGTTATAAATCGC 59.128 55.000 0.00 0.00 35.12 4.58
696 773 2.536761 TCCCGCCAGGTTATAAATCG 57.463 50.000 0.00 0.00 36.75 3.34
697 774 2.882761 GGTTCCCGCCAGGTTATAAATC 59.117 50.000 0.00 0.00 36.75 2.17
698 775 2.242708 TGGTTCCCGCCAGGTTATAAAT 59.757 45.455 0.00 0.00 36.75 1.40
699 776 1.634459 TGGTTCCCGCCAGGTTATAAA 59.366 47.619 0.00 0.00 36.75 1.40
700 777 1.287217 TGGTTCCCGCCAGGTTATAA 58.713 50.000 0.00 0.00 36.75 0.98
701 778 1.210967 CTTGGTTCCCGCCAGGTTATA 59.789 52.381 0.00 0.00 40.01 0.98
702 779 0.034477 CTTGGTTCCCGCCAGGTTAT 60.034 55.000 0.00 0.00 40.01 1.89
703 780 1.377229 CTTGGTTCCCGCCAGGTTA 59.623 57.895 0.00 0.00 40.01 2.85
724 801 1.938585 TATCGCTCTAGGGAATGGGG 58.061 55.000 0.00 0.00 40.44 4.96
758 835 7.916977 GGGTTTATATCGGTTTAGCGAATTTTT 59.083 33.333 8.17 0.00 0.00 1.94
766 843 6.073385 GCTACAAGGGTTTATATCGGTTTAGC 60.073 42.308 0.00 0.00 0.00 3.09
791 868 5.940470 CCCATTTATTAGCTAGCTAACCCAG 59.060 44.000 33.80 22.59 40.76 4.45
792 869 5.747842 GCCCATTTATTAGCTAGCTAACCCA 60.748 44.000 33.80 21.91 40.76 4.51
793 870 4.700692 GCCCATTTATTAGCTAGCTAACCC 59.299 45.833 33.80 14.95 40.76 4.11
794 871 5.412904 CAGCCCATTTATTAGCTAGCTAACC 59.587 44.000 33.80 16.57 40.76 2.85
795 872 5.412904 CCAGCCCATTTATTAGCTAGCTAAC 59.587 44.000 33.80 20.41 40.76 2.34
796 873 5.560724 CCAGCCCATTTATTAGCTAGCTAA 58.439 41.667 33.35 33.35 41.95 3.09
797 874 4.565652 GCCAGCCCATTTATTAGCTAGCTA 60.566 45.833 20.67 20.67 37.08 3.32
798 875 3.812167 GCCAGCCCATTTATTAGCTAGCT 60.812 47.826 23.12 23.12 37.08 3.32
799 876 2.489722 GCCAGCCCATTTATTAGCTAGC 59.510 50.000 6.62 6.62 33.09 3.42
800 877 3.084786 GGCCAGCCCATTTATTAGCTAG 58.915 50.000 0.00 0.00 33.33 3.42
801 878 3.154827 GGCCAGCCCATTTATTAGCTA 57.845 47.619 0.00 0.00 33.33 3.32
802 879 2.001076 GGCCAGCCCATTTATTAGCT 57.999 50.000 0.00 0.00 35.52 3.32
852 929 0.550914 AGGCGATTCCCTATTTGCCA 59.449 50.000 3.68 0.00 39.35 4.92
909 989 2.758648 GACCAATTTGGGCCCTGTT 58.241 52.632 25.70 12.22 40.64 3.16
923 1003 2.224159 GGACTGGCTTGAGGGACCA 61.224 63.158 0.00 0.00 0.00 4.02
925 1005 2.224159 TGGGACTGGCTTGAGGGAC 61.224 63.158 0.00 0.00 0.00 4.46
1059 1148 4.269523 GCCATGCGGGAGGCCATA 62.270 66.667 5.01 0.00 45.18 2.74
1172 1261 4.240888 TGAGAAGAGAAATGAACGAGCAG 58.759 43.478 0.00 0.00 0.00 4.24
1178 1267 5.123027 AGCCGAAATGAGAAGAGAAATGAAC 59.877 40.000 0.00 0.00 0.00 3.18
1190 1279 2.859165 AAGGTGAAGCCGAAATGAGA 57.141 45.000 0.00 0.00 43.70 3.27
1193 1282 3.621715 GGTAGTAAGGTGAAGCCGAAATG 59.378 47.826 0.00 0.00 43.70 2.32
1195 1284 2.353011 CGGTAGTAAGGTGAAGCCGAAA 60.353 50.000 0.00 0.00 43.70 3.46
1205 1294 1.963857 GCTTCCCCTCGGTAGTAAGGT 60.964 57.143 0.00 0.00 0.00 3.50
1264 1353 1.628846 GTTCTCCTAGGGTTGAAGCCA 59.371 52.381 16.56 0.95 38.48 4.75
1396 1486 8.256356 ACATAAGGAGTAGCATCTAAACTGAT 57.744 34.615 0.00 0.00 0.00 2.90
1459 1549 1.671054 GCCAAAGCAGCCTACGTGA 60.671 57.895 0.00 0.00 39.53 4.35
1462 1552 2.456119 CGAGCCAAAGCAGCCTACG 61.456 63.158 0.00 0.00 43.56 3.51
1610 1700 6.582677 TGAAACTTCAGAAAACCACAGAAA 57.417 33.333 0.00 0.00 32.50 2.52
1679 1769 7.954666 AAGCCATTTTGCTATTTACTAGGAA 57.045 32.000 0.00 0.00 41.80 3.36
1726 1818 8.997621 TCCGATATTAGAAGCAATACCAATAC 57.002 34.615 0.00 0.00 0.00 1.89
1727 1819 9.031537 TCTCCGATATTAGAAGCAATACCAATA 57.968 33.333 0.00 0.00 0.00 1.90
1728 1820 7.907389 TCTCCGATATTAGAAGCAATACCAAT 58.093 34.615 0.00 0.00 0.00 3.16
1729 1821 7.297936 TCTCCGATATTAGAAGCAATACCAA 57.702 36.000 0.00 0.00 0.00 3.67
1730 1822 6.911250 TCTCCGATATTAGAAGCAATACCA 57.089 37.500 0.00 0.00 0.00 3.25
1731 1823 9.303537 GTTATCTCCGATATTAGAAGCAATACC 57.696 37.037 0.00 0.00 0.00 2.73
1744 1836 6.085555 ACGTGAATGTGTTATCTCCGATAT 57.914 37.500 0.00 0.00 0.00 1.63
1749 1841 7.997107 TTATGTACGTGAATGTGTTATCTCC 57.003 36.000 0.00 0.00 0.00 3.71
1780 1872 2.355010 AGAAAGTGTTGCCTCTTGCT 57.645 45.000 0.00 0.00 42.00 3.91
1781 1873 4.773323 AATAGAAAGTGTTGCCTCTTGC 57.227 40.909 0.00 0.00 41.77 4.01
1782 1874 5.617751 CGGAAATAGAAAGTGTTGCCTCTTG 60.618 44.000 0.00 0.00 0.00 3.02
1789 1881 6.142320 GCAAGAAACGGAAATAGAAAGTGTTG 59.858 38.462 0.00 0.00 0.00 3.33
1795 1887 7.033530 TCTTTGCAAGAAACGGAAATAGAAA 57.966 32.000 0.00 0.00 33.83 2.52
1935 2041 5.351458 GCATGAAAGGGGTCAATAATTCAC 58.649 41.667 0.00 0.00 30.46 3.18
1952 2058 4.053983 GAGATAATCTGACAGCGCATGAA 58.946 43.478 11.47 0.00 0.00 2.57
1959 2065 5.465051 TCAATAGCGAGATAATCTGACAGC 58.535 41.667 0.00 0.00 0.00 4.40
1970 2080 9.994957 TCAAACCATGATGCTCAATAGCGAGAT 62.995 40.741 0.00 0.00 41.84 2.75
1975 2085 4.906065 TCAAACCATGATGCTCAATAGC 57.094 40.909 0.00 0.00 40.36 2.97
1999 2109 6.430616 TGATGATTGTAATGCTTGACAGACAA 59.569 34.615 0.00 0.00 40.43 3.18
2001 2111 6.426980 TGATGATTGTAATGCTTGACAGAC 57.573 37.500 0.00 0.00 0.00 3.51
2002 2112 6.459161 GCATGATGATTGTAATGCTTGACAGA 60.459 38.462 0.00 0.00 41.71 3.41
2003 2113 5.685954 GCATGATGATTGTAATGCTTGACAG 59.314 40.000 0.00 0.00 41.71 3.51
2022 2132 6.372937 TACACCGAAATGTAAAATCAGCATGA 59.627 34.615 0.00 0.00 40.02 3.07
2034 2144 6.381994 AGGGAGTAATTCTACACCGAAATGTA 59.618 38.462 0.00 0.00 39.10 2.29
2035 2145 5.189145 AGGGAGTAATTCTACACCGAAATGT 59.811 40.000 0.00 0.00 39.10 2.71
2104 2216 5.999205 ATTTTTGTCATAGACATGGCCAA 57.001 34.783 10.96 0.00 42.40 4.52
2184 2300 7.499321 ACATCGACAACACCAAATTTACTTA 57.501 32.000 0.00 0.00 0.00 2.24
2188 2304 6.378710 TCAACATCGACAACACCAAATTTA 57.621 33.333 0.00 0.00 0.00 1.40
2284 2403 6.694877 AAAGTACTCCCTCAGTTTCAAAAC 57.305 37.500 0.00 0.00 36.43 2.43
2294 2413 7.786046 TCAGTATGTTAAAAGTACTCCCTCA 57.214 36.000 0.00 0.00 37.40 3.86
2321 2462 2.029838 AGCTAGCAGCATACACAACC 57.970 50.000 18.83 0.00 45.56 3.77
2399 2540 9.674068 AAGGCCAAGTAAGAAACAAAATAAAAA 57.326 25.926 5.01 0.00 0.00 1.94
2451 2592 4.437820 GTCTTGCGTTTCATGTTCTTTGAC 59.562 41.667 0.00 0.00 0.00 3.18
2556 2697 5.886609 TCACAATTTTCCTAGTTCCCATCA 58.113 37.500 0.00 0.00 0.00 3.07
2570 2711 9.724839 CAAGAAAGAAATTTGCATCACAATTTT 57.275 25.926 7.95 0.00 41.92 1.82
2676 2817 4.410228 CCATCAAGAAAGATACTCCCTCCA 59.590 45.833 0.00 0.00 0.00 3.86
2952 3095 1.673665 CCAGGCTCCACAGACTTGC 60.674 63.158 0.00 0.00 34.70 4.01
2980 3123 1.672356 ACAGGGCACGACTGCATTC 60.672 57.895 0.11 0.00 46.28 2.67
3067 3210 5.755861 GCAAAAAGATCTACCTGGCTACTAG 59.244 44.000 0.00 0.00 0.00 2.57
3068 3211 5.425539 AGCAAAAAGATCTACCTGGCTACTA 59.574 40.000 0.00 0.00 0.00 1.82
3069 3212 4.226168 AGCAAAAAGATCTACCTGGCTACT 59.774 41.667 0.00 0.00 0.00 2.57
3092 3235 1.348064 AGGAGAAATGGTGTCGGTCA 58.652 50.000 0.00 0.00 0.00 4.02
3159 3547 7.390027 ACACTGAAATCAATCTTAGTAGTGCT 58.610 34.615 0.00 0.00 37.19 4.40
3162 3550 8.812972 TGGTACACTGAAATCAATCTTAGTAGT 58.187 33.333 0.00 0.00 0.00 2.73
3187 3575 2.104281 TCCTGCATCATGAGATCCAGTG 59.896 50.000 0.09 0.00 38.19 3.66
3304 5201 5.352016 TGCCGCGTTCTAGTTATTTACATTT 59.648 36.000 4.92 0.00 0.00 2.32
3388 5285 7.387397 TGCTGAAGAAATCAAAGTTGTTGTTTT 59.613 29.630 0.00 0.00 37.67 2.43
3389 5286 6.873076 TGCTGAAGAAATCAAAGTTGTTGTTT 59.127 30.769 0.00 0.00 37.67 2.83
3390 5287 6.397272 TGCTGAAGAAATCAAAGTTGTTGTT 58.603 32.000 0.00 0.00 37.67 2.83
3391 5288 5.964758 TGCTGAAGAAATCAAAGTTGTTGT 58.035 33.333 0.00 0.00 37.67 3.32
3392 5289 6.890663 TTGCTGAAGAAATCAAAGTTGTTG 57.109 33.333 0.00 0.00 37.67 3.33
3393 5290 8.392612 CAATTTGCTGAAGAAATCAAAGTTGTT 58.607 29.630 0.00 0.00 37.67 2.83
3394 5291 7.011669 CCAATTTGCTGAAGAAATCAAAGTTGT 59.988 33.333 0.00 0.00 37.67 3.32
3395 5292 7.349711 CCAATTTGCTGAAGAAATCAAAGTTG 58.650 34.615 0.00 0.00 37.67 3.16
3396 5293 6.017687 GCCAATTTGCTGAAGAAATCAAAGTT 60.018 34.615 0.00 0.00 37.67 2.66
3449 5346 0.313672 GATGGAGTAGGAGAGCTGCG 59.686 60.000 0.00 0.00 0.00 5.18
3619 5516 0.738389 ACACCGCAAAGTTCAACCTG 59.262 50.000 0.00 0.00 0.00 4.00
3832 5729 0.318360 CGGTGCAGTTCGACTACACA 60.318 55.000 15.57 1.40 42.77 3.72
3907 5804 1.135094 CCATCCTCCAGGCACACTAT 58.865 55.000 0.00 0.00 34.44 2.12


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.